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- PDB-2xwb: Crystal Structure of Complement C3b in complex with Factors B and D -

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Basic information

Entry
Database: PDB / ID: 2xwb
TitleCrystal Structure of Complement C3b in complex with Factors B and D
Components
  • (COMPLEMENT C3B ...) x 2
  • (COMPLEMENT FACTOR ...) x 2
KeywordsHYDROLASE / IMMUNE SYSTEM / PRO-CONVERTASE / SERINE PROTEASE / CONFORMATIONAL CHANGES / ALTERNATIVE PATHWAY
Function / homology
Function and homology information


alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement factor D / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance ...alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement factor D / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / serine-type peptidase activity / Peptide ligand-binding receptors / platelet alpha granule lumen / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / Platelet degranulation / G alpha (i) signalling events / secretory granule lumen / ficolin-1-rich granule lumen / blood microparticle / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 ...Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement Module, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Complement Module; domain 1 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / von Willebrand factor, type A domain / Other non-globular / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Single Sheet / von Willebrand factor A-like domain superfamily / Special / Ribbon / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Jelly Rolls / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Complement factor D / Complement factor B / Complement C3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsForneris, F. / Ricklin, D. / Wu, J. / Tzekou, A. / Wallace, R.S. / Lambris, J.D. / Gros, P.
CitationJournal: Science / Year: 2010
Title: Structures of C3B in Complex with Factors B and D Give Insight Into Complement Convertase Formation.
Authors: Forneris, F. / Ricklin, D. / Wu, J. / Tzekou, A. / Wallace, R.S. / Lambris, J.D. / Gros, P.
History
DepositionNov 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Non-polymer description ...Database references / Non-polymer description / Other / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT C3B BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
C: COMPLEMENT C3B BETA CHAIN
D: COMPLEMENT C3B ALPHA' CHAIN
F: COMPLEMENT FACTOR B
H: COMPLEMENT FACTOR B
I: COMPLEMENT FACTOR D
J: COMPLEMENT FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)566,82024
Polymers562,9878
Non-polymers3,83416
Water724
1
A: COMPLEMENT C3B BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
F: COMPLEMENT FACTOR B
J: COMPLEMENT FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,51212
Polymers281,4934
Non-polymers2,0188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18399 Å2
ΔGint-56.3 kcal/mol
Surface area107470 Å2
2
C: COMPLEMENT C3B BETA CHAIN
D: COMPLEMENT C3B ALPHA' CHAIN
H: COMPLEMENT FACTOR B
I: COMPLEMENT FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,30912
Polymers281,4934
Non-polymers1,8158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18198 Å2
ΔGint-60.7 kcal/mol
Surface area107122 Å2
3
C: COMPLEMENT C3B BETA CHAIN
D: COMPLEMENT C3B ALPHA' CHAIN
H: COMPLEMENT FACTOR B
J: COMPLEMENT FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,30912
Polymers281,4934
Non-polymers1,8158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20110 Å2
ΔGint-99.3 kcal/mol
Surface area131690 Å2
MethodPISA
4
A: COMPLEMENT C3B BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
F: COMPLEMENT FACTOR B
I: COMPLEMENT FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,51212
Polymers281,4934
Non-polymers2,0188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20150 Å2
ΔGint-98.9 kcal/mol
Surface area131900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.275, 135.775, 149.975
Angle α, β, γ (deg.)95.47, 110.69, 113.39
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29
110
210
111
211
112
212
113
213
114
214

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A OR CHAIN B AND (RESSEQ 744:804 )
211CHAIN C OR CHAIN D AND (RESSEQ 744:804 )
112CHAIN B AND (RESSEQ 805:900 )
212CHAIN D AND (RESSEQ 805:900 )
113CHAIN B AND (RESSEQ 913:965 OR RESSEQ 1268:1331 )
213CHAIN D AND (RESSEQ 913:965 OR RESSEQ 1268:1331 )
114CHAIN B AND (RESSEQ 969:1102 )
214CHAIN D AND (RESSEQ 969:1102 )
115CHAIN B AND (RESSEQ 1108:1264 )
215CHAIN D AND (RESSEQ 1108:1264 )
116CHAIN B AND (RESSEQ 1332:1480 )
216CHAIN D AND (RESSEQ 1332:1480 )
117CHAIN B AND (RESSEQ 1485:1531 )
217CHAIN D AND (RESSEQ 1485:1531 )
118CHAIN B AND (RESSEQ 1538:1641 )
218CHAIN D AND (RESSEQ 1538:1641 )
119CHAIN F AND (RESSEQ 10:75 )
219CHAIN H AND (RESSEQ 10:75 )
1110CHAIN F AND (RESSEQ 78:220 )
2110CHAIN H AND (RESSEQ 78:220 )
1111CHAIN F AND (RESSEQ 244:340 )
2111CHAIN H AND (RESSEQ 244:340 )
1112CHAIN F AND (RESSEQ 358:460 )
2112CHAIN H AND (RESSEQ 358:460 )
1113CHAIN F AND (RESSEQ 485:741 )
2113CHAIN H AND (RESSEQ 485:741 )
1114CHAIN J
2114CHAIN I

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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Components

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COMPLEMENT C3B ... , 2 types, 4 molecules ACBD

#1: Protein COMPLEMENT C3B BETA CHAIN


Mass: 71154.047 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-664 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: BLOOD / Tissue: PLASMA / References: UniProt: P01024
#2: Protein COMPLEMENT C3B ALPHA' CHAIN


Mass: 103759.797 Da / Num. of mol.: 2 / Fragment: RESIDUES 752-1663 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: BLOOD / Tissue: PLASMA / References: UniProt: P01024

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COMPLEMENT FACTOR ... , 2 types, 4 molecules FHIJ

#3: Protein COMPLEMENT FACTOR B / C3/C5 CONVERTASE / GLYCINE-RICH BETA GLYCOPROTEIN / GBG / PBF2 / PROPERDIN FACTOR B


Mass: 82156.672 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-764 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Organ: BLOOD / Plasmid: PUPE.06.08 / Cell line (production host): HEK293-ES / Production host: HOMO SAPIENS (human)
References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase
#4: Protein COMPLEMENT FACTOR D


Mass: 24422.807 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Organ: BLOOD / Plasmid: PUPE.05.05 / Cell line (production host): HEK293-ES / Production host: HOMO SAPIENS (human) / References: UniProt: P00746, complement factor D

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Sugars , 3 types, 10 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 10 molecules

#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN F, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN F, ASN 285 TO ASP ...ENGINEERED RESIDUE IN CHAIN F, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN F, ASN 285 TO ASP ENGINEERED RESIDUE IN CHAIN H, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN H, ASN 285 TO ASP ENGINEERED RESIDUE IN CHAIN I, SER 208 TO ALA ENGINEERED RESIDUE IN CHAIN J, SER 208 TO ALA
Sequence detailsRESIDUE 991 HAS BEEN CONVERTED FROM GLN TO GLU IN THE CONVERSION OF C3 TO C3B.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.5 % / Description: NONE
Crystal growpH: 7.7 / Details: PH 7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.5→67.42 Å / Num. obs: 88224 / % possible obs: 99.2 % / Observed criterion σ(I): 3.5 / Redundancy: 3.3 % / Biso Wilson estimate: 83.14 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.8
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A74

2a74


Resolution: 3.49→65.95 Å / SU ML: 0.46 / σ(F): 2.01 / Phase error: 24.08 / Stereochemistry target values: ML
Details: WATER MOLECULES HAVE BEEN INCLUDED ONLY TO COMPLETE THE COORDINATION OF THE MG2+ ION IN THE MIDAS SITE
RfactorNum. reflection% reflection
Rfree0.244 4427 5 %
Rwork0.189 --
obs0.192 88180 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.14 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 114.37 Å2
Baniso -1Baniso -2Baniso -3
1--10.2414 Å211.8086 Å2-8.8541 Å2
2---4.0625 Å2-5.1292 Å2
3---2.7506 Å2
Refinement stepCycle: LAST / Resolution: 3.49→65.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39033 0 248 4 39285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00240171
X-RAY DIFFRACTIONf_angle_d0.48854375
X-RAY DIFFRACTIONf_dihedral_angle_d11.11114898
X-RAY DIFFRACTIONf_chiral_restr0.0576102
X-RAY DIFFRACTIONf_plane_restr0.0027022
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5020X-RAY DIFFRACTIONPOSITIONAL
12C5020X-RAY DIFFRACTIONPOSITIONAL0.05
21B790X-RAY DIFFRACTIONPOSITIONAL
22D790X-RAY DIFFRACTIONPOSITIONAL0.027
31B908X-RAY DIFFRACTIONPOSITIONAL
32D908X-RAY DIFFRACTIONPOSITIONAL0.084
41B1048X-RAY DIFFRACTIONPOSITIONAL
42D1048X-RAY DIFFRACTIONPOSITIONAL0.026
51B1238X-RAY DIFFRACTIONPOSITIONAL
52D1238X-RAY DIFFRACTIONPOSITIONAL0.021
61B1133X-RAY DIFFRACTIONPOSITIONAL
62D1133X-RAY DIFFRACTIONPOSITIONAL0.02
71B370X-RAY DIFFRACTIONPOSITIONAL
72D370X-RAY DIFFRACTIONPOSITIONAL0.1
81B849X-RAY DIFFRACTIONPOSITIONAL
82D849X-RAY DIFFRACTIONPOSITIONAL0.028
91F509X-RAY DIFFRACTIONPOSITIONAL
92H509X-RAY DIFFRACTIONPOSITIONAL0.02
101F1115X-RAY DIFFRACTIONPOSITIONAL
102H1115X-RAY DIFFRACTIONPOSITIONAL0.027
111F752X-RAY DIFFRACTIONPOSITIONAL
112H752X-RAY DIFFRACTIONPOSITIONAL0.033
121F830X-RAY DIFFRACTIONPOSITIONAL
122H830X-RAY DIFFRACTIONPOSITIONAL0.029
131F2030X-RAY DIFFRACTIONPOSITIONAL
132H2030X-RAY DIFFRACTIONPOSITIONAL0.075
141J1710X-RAY DIFFRACTIONPOSITIONAL
142I1710X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.493-3.53270.37371480.30022283X-RAY DIFFRACTION84
3.5327-3.57430.34611890.28552797X-RAY DIFFRACTION99
3.5743-3.61780.32841480.27122787X-RAY DIFFRACTION99
3.6178-3.66360.30961310.26272859X-RAY DIFFRACTION99
3.6636-3.71180.32341290.24722806X-RAY DIFFRACTION99
3.7118-3.76270.30771490.24422777X-RAY DIFFRACTION99
3.7627-3.81640.27531470.22312783X-RAY DIFFRACTION99
3.8164-3.87340.29411370.21792875X-RAY DIFFRACTION99
3.8734-3.93390.27511480.21132782X-RAY DIFFRACTION99
3.9339-3.99840.26111400.20172827X-RAY DIFFRACTION99
3.9984-4.06730.2241330.19422776X-RAY DIFFRACTION99
4.0673-4.14130.26331470.18292823X-RAY DIFFRACTION99
4.1413-4.22090.25861450.17072800X-RAY DIFFRACTION99
4.2209-4.30710.2081610.1672836X-RAY DIFFRACTION99
4.3071-4.40070.2481420.16192801X-RAY DIFFRACTION99
4.4007-4.5030.18791290.15282833X-RAY DIFFRACTION99
4.503-4.61560.20261360.14862777X-RAY DIFFRACTION99
4.6156-4.74040.2191350.14452860X-RAY DIFFRACTION99
4.7404-4.87980.20441670.14242806X-RAY DIFFRACTION99
4.8798-5.03730.18691800.14192775X-RAY DIFFRACTION99
5.0373-5.21730.19431540.14152798X-RAY DIFFRACTION99
5.2173-5.42610.19471520.15242815X-RAY DIFFRACTION99
5.4261-5.67290.22221590.15932810X-RAY DIFFRACTION99
5.6729-5.97180.2171440.16422820X-RAY DIFFRACTION99
5.9718-6.34570.1941330.1682801X-RAY DIFFRACTION99
6.3457-6.83510.25321510.17252838X-RAY DIFFRACTION99
6.8351-7.52210.23791420.17192810X-RAY DIFFRACTION99
7.5221-8.60850.23881410.16822808X-RAY DIFFRACTION100
8.6085-10.83810.1881600.15892813X-RAY DIFFRACTION99
10.8381-65.96580.24911500.222777X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.05470.7499-0.30370.6370.25530.3580.3476-0.4663-0.45930.1559-0.1931-0.2842-0.19940.0552-0.16360.5829-0.21110.11370.6596-0.19071.202885.4108-95.20444.3835
21.17740.16130.61030.0291-0.02010.16190.00330.2054-0.399-0.0405-0.0380.1639-0.0951-0.01810.03330.3294-0.21470.0380.6374-0.25380.349469.5548-57.11710.1669
30.15590.0870.53422.1061.12532.02470.2741-0.7097-0.1416-0.3748-0.07660.806-0.2446-0.3597-0.08620.4395-0.3588-0.13751.008-0.17810.668145.033-51.1066-13.8188
40.71511.1130.39322.51640.46570.07430.11440.2294-0.1554-0.2356-0.32930.49690.1435-0.35150.18240.7433-0.4219-0.07341.1031-0.16871.117347.9218-85.3976-6.7193
51.20640.33570.4850.12980.28420.66910.4794-0.0399-0.94640.5186-0.3779-0.12940.1642-0.1263-0.14840.8906-0.50480.13440.7156-0.07221.410462.4122-97.6287.5642
63.12882.1764-0.49471.7983-0.84771.01850.09750.333-0.56850.12570.2231-0.4601-0.4648-0.3361-0.0950.5494-0.42130.39830.7903-0.17640.556657.5733-54.58624.7416
70.81510.2953-0.02430.8468-0.77980.7216-0.1715-0.3723-0.5320.32430.23080.07790.1922-0.39340.07770.0196-0.41660.05880.177-0.04650.381368.7179-74.4444.1703
80.9717-0.50550.30791.23970.1211-0.1550.14750.35770.1218-0.0738-0.13170.2941-0.0056-0.41370.11360.0698-0.07-0.01510.4852-0.1005-0.017769.0099-36.53156.0121
91.2230.3827-0.80781.82420.433.49330.15870.3566-0.2984-0.3296-0.13590.43910.296-0.4511-0.10990.43590.0322-0.15980.377-0.04380.4541110.7906-94.4691-23.1379
100.5420.36780.23480.33530.27530.92120.11910.7847-0.12090.1320.1439-0.4677-0.13770.027-0.04270.1980.00370.1690.867-0.11380.049294.64-45.2274-13.8302
111.10880.94021.40321.74790.38083.0042-0.22440.13950.4983-0.22060.03820.7436-0.0376-0.6050.15080.28130.0969-0.18720.90980.01010.515850.2976-20.7993-8.2497
121.55190.29360.30980.5748-0.76682.27440.080.0080.7896-0.1523-0.2741-0.0827-0.42720.15960.24240.70610.1383-0.25120.23960.09050.552379.25138.13883.5686
130.6298-0.0388-0.3541.00311.21231.54990.4330.37260.15750.81510.192-0.53080.0904-0.7271-0.67990.94690.34950.37230.40450.35661.3689156.3188-99.65962.5558
140.5099-0.171-0.10440.19860.15440.57110.0731-0.3865-0.4318-0.18420.2135-0.2904-0.34910.4290.39180.77240.6863-0.11680.44220.1560.2445157.4133-65.676177.6229
150.66760.4750.59830.4109-0.13712.10780.04210.3443-0.32850.20020.2615-0.3318-0.32680.1849-0.18520.46470.4783-0.17160.7896-0.10370.4067191.3676-58.923991.0558
160.1904-0.1522-0.15272.44650.41430.0823-0.0304-0.43970.0170.2705-0.1255-0.91660.23470.03630.10771.22460.5994-0.17931.0492-0.05971.132191.1889-87.072176.4315
171.9304-1.63740.3441.3275-0.2788-0.0481-0.0124-0.122-0.57050.2292-0.00960.4855-0.18710.19080.01710.94490.50350.22470.55810.05530.6843178.3102-95.901658.7406
180.4537-0.791-0.93811.41251.68121.99910.10350.1456-0.0181-0.239-0.3545-0.1094-0.1671-0.72060.20631.78190.45190.74851.77570.02751.4022180.2121-45.026455.547
190.2086-0.5774-0.3582.52710.56020.4154-0.3979-0.2291-0.2021-0.32870.323-0.0960.21780.21870.12710.72120.57140.0970.69770.05580.44170.0721-77.495169.8047
200.97450.2851-0.05870.49150.28120.63920.1188-0.51380.0728-0.00760.0430.00210.44740.7299-0.0610.47310.2853-0.07730.6614-0.03410.1317164.2821-42.12980.292
210.50310.49170.8162.348-0.02391.8080.15140.0494-0.0837-0.16340.32850.48290.4106-1.0805-0.44371.344-0.1590.09881.2850.07341.571134.3229-112.280290.9892
221-0.5578-0.28830.4381-0.08220.59050.0552-0.44980.0685-0.05990.24670.1441-0.17540.369-0.12360.3930.1165-0.01110.6270.13020.2333141.2915-58.941795.995
230.8076-0.6877-0.04081.25180.10290.9451-0.055-0.18210.18970.36980.0979-0.35390.18220.756-0.10320.24440.1284-0.10641.0097-0.21410.1892181.043-29.105199.1944
240.14-0.0418-0.00760.72630.80581.2401-0.0083-0.13670.18860.22150.2545-0.2910.16840.3513-0.21350.2796-0.0293-0.00720.3436-0.1810.26148.1977-1.620795.9749
252.1568-1.8331-0.42342.14410.45620.2881-0.10220.5858-0.70040.38840.11370.2499-0.5068-0.49330.17420.2960.1680.12420.6805-0.41660.584377.6498-2.110137.5645
260.5912-0.4551-0.11630.4077-0.05210.2502-0.2475-0.07850.07060.159-0.0010.0385-0.2869-0.50090.08960.55630.1978-0.09920.914-0.15080.53478.2876-6.924531.2691
272.999-0.3960.1610.94340.03180.0141-0.40710.0730.1384-0.42470.54460.14690.21940.7139-0.10551.23990.12420.08341.3028-0.30560.460671.6448-10.140122.5855
281.1661.54531.4722.53011.57482.2652-0.2927-0.1064-0.0119-0.0953-0.14950.47110.2786-1.02040.09880.2305-0.22440.04640.5230.02980.247475.8732-34.962824.8998
290.89910.3283-0.82940.4314-0.22550.8658-0.03540.29790.1595-0.3288-0.16990.08240.0079-0.9247-0.64380.1625-0.1250.17670.52570.10240.013486.7334-33.171614.3609
300.16260.10430.00720.621-0.03010.1731-0.2033-0.20460.06240.0187-0.16550.46570.0631-0.2674-0.87250.1794-0.27340.2785-0.21460.7024-0.1898105.4941-24.783623.2683
311.6935-0.3809-0.03542.11390.51721.38040.13940.42190.1471-0.3131-0.1993-0.1512-0.3876-0.2405-0.12420.3143-0.08290.04580.240.12670.0612104.7127-11.547818.0242
321.94110.42350.82591.06650.03871.4658-0.00360.3933-0.31670.00720.02480.02930.24370.3011-0.01780.1322-0.06980.08710.1926-0.07740.294114.4836-51.899311.9449
331.04361.45240.46272.27060.14451.2774-0.29240.13530.4558-0.1812-0.0915-0.6159-0.67770.88110.35660.5222-0.1875-0.09990.79240.09380.7982150.7397-5.09363.3619
342.0251.1939-2.1341.3146-1.16272.3168-0.33080.06950.46330.11710.5384-0.08430.7053-0.8843-0.08311.1582-0.3523-0.19941.5908-0.01790.6747157.7806-12.415672.5605
352.301-0.28650.41530.0414-0.04460.9463-0.03010.17250.07340.009-0.0123-0.07080.47221.05870.04970.30680.3289-0.06050.7128-0.14840.3049157.8688-32.900563.8362
360.45430.37940.30040.66220.28580.2273-0.34020.5203-0.11260.53110.58210.01910.28990.2003-0.21660.54040.34810.13670.8771-0.00980.3288149.974-41.074162.0204
371.3938-0.22940.11060.9313-0.09680.25650.0941-0.5692-0.05060.27220.1812-0.17790.51550.7364-0.16550.47410.16110.05610.5795-0.03070.0633145.3302-36.967676.5563
380.1696-0.2363-0.41240.85551.23181.88080.0188-0.07090.02910.4030.2013-0.00510.71740.12880.16510.20820.19770.1171-0.2983-0.5076-0.5283124.5662-31.194667.1208
391.0788-0.26230.52561.250.00650.74630.1278-0.2230.13390.1609-0.14540.06880.0407-0.10880.07030.30040.07460.10010.243-0.03810.0195125.5464-19.459574.9294
401.9911-0.09680.33070.42930.26821.73320.0357-0.1414-0.5466-0.20510.04770.1170.645-0.1108-0.07250.74270.0961-0.04710.1483-0.00260.5058121.1442-60.853668.7665
411.22240.40251.06060.32720.40291.6738-0.543-0.02490.656-0.1408-0.24260.0385-0.10030.00310.49160.4129-0.0514-0.04010.2903-0.19640.464592.1157-16.196353.8156
421.21840.1744-0.11240.1625-0.3671.1951-0.2462-0.61650.0937-0.0414-0.05960.01921.16960.22930.39160.91670.17070.1471.3197-0.12030.677488.6528-22.55770.1836
430.74090.16280.80751.43810.96852.5284-0.2523-0.25310.32450.0927-0.4491-0.0858-0.0692-0.79440.49840.27020.1402-0.03140.4306-0.19610.328391.1025-19.302753.1206
441.84021.13961.28920.82870.36881.960.4856-0.6633-0.27150.3668-0.2941-0.55480.6965-0.61980.17680.4008-0.00130.20460.3579-0.0478-0.162996.4693-32.043951.1088
450.61230.658-0.0640.7779-0.2331.4174-0.2-0.21550.12290.1876-0.2948-0.4463-0.51090.15420.36750.443-0.126-0.11320.44430.19070.5818138.0311-11.261640.283
462.0411-0.9110.65660.4169-0.2690.2688-0.14470.91760.26210.0155-0.4798-0.1986-0.0360.71790.49650.9887-0.29280.14011.47130.37981.1628141.9554-11.983722.8346
472.07660.48471.19051.0533-0.51731.4344-0.29480.39410.61630.1177-0.21010.0869-0.31930.27980.38090.1992-0.1309-0.030.22190.08160.3015137.4753-18.794739.6939
480.30570.20590.36150.68630.41750.42810.4802-0.1693-0.00730.29-0.61480.22610.24220.1249-0.06070.4761-0.07040.08530.43810.26670.0364138.7125-25.884436.6109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:105)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 106:245)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 246:317)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 318:431)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 432:539)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 540:552)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 553:642)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 730:966)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 967:1266)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 1267:1334)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 1335:1499)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 1500:1641)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 1:105)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 106:207)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 208:310)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 311:442)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 443:545)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 546:551)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 552:642)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 730:966)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 967:1267)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 1268:1336)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 1337:1499)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 1500:1641)
25X-RAY DIFFRACTION25(CHAIN F AND RESID 10:30)
26X-RAY DIFFRACTION26(CHAIN F AND RESID 31:62)
27X-RAY DIFFRACTION27(CHAIN F AND RESID 63:70)
28X-RAY DIFFRACTION28(CHAIN F AND RESID 71:108)
29X-RAY DIFFRACTION29(CHAIN F AND RESID 109:198)
30X-RAY DIFFRACTION30(CHAIN F AND RESID 199:223)
31X-RAY DIFFRACTION31(CHAIN F AND RESID 240:447)
32X-RAY DIFFRACTION32(CHAIN F AND RESID 448:741)
33X-RAY DIFFRACTION33(CHAIN H AND RESID 10:62)
34X-RAY DIFFRACTION34(CHAIN H AND RESID 63:70)
35X-RAY DIFFRACTION35(CHAIN H AND RESID 71:96)
36X-RAY DIFFRACTION36(CHAIN H AND RESID 97:136)
37X-RAY DIFFRACTION37(CHAIN H AND RESID 137:200)
38X-RAY DIFFRACTION38(CHAIN H AND RESID 201:223)
39X-RAY DIFFRACTION39(CHAIN H AND RESID 240:451)
40X-RAY DIFFRACTION40(CHAIN H AND RESID 452:741)
41X-RAY DIFFRACTION41(CHAIN I AND RESID 1:42)
42X-RAY DIFFRACTION42(CHAIN I AND RESID 43:48)
43X-RAY DIFFRACTION43(CHAIN I AND RESID 49:150)
44X-RAY DIFFRACTION44(CHAIN I AND RESID 151:228)
45X-RAY DIFFRACTION45(CHAIN J AND RESID 1:42)
46X-RAY DIFFRACTION46(CHAIN J AND RESID 43:48)
47X-RAY DIFFRACTION47(CHAIN J AND RESID 49:197)
48X-RAY DIFFRACTION48(CHAIN J AND RESID 198:227)

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